From: paradis <paradis@6e262413-ae40-0410-9e79-b911bd7a66b7>
Date: Tue, 10 Nov 2009 04:36:40 +0000 (+0000)
Subject: removing plot.phylo.coor (definitely)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=a896dd1b852fde1e90b43d94ffca2301f178507f;p=ape.git

removing plot.phylo.coor (definitely)


git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@99 6e262413-ae40-0410-9e79-b911bd7a66b7
---

diff --git a/R/plot.phylo.coor.R b/R/plot.phylo.coor.R
deleted file mode 100644
index 5794af4..0000000
--- a/R/plot.phylo.coor.R
+++ /dev/null
@@ -1,134 +0,0 @@
-## plot.phylo.coor.R (2008-04-14)
-
-##   Coordinates of a Tree Plot
-
-## Copyright 2008 Damien de Vienne
-
-## This file is part of the R-package `ape'.
-## See the file ../COPYING for licensing issues.
-
-plot.phylo.coor <-
-    function (x, type = "phylogram", use.edge.length = TRUE, node.pos = NULL,
-              direction = "rightwards", ...)
-{
-    Ntip <- length(x$tip.label)
-    if (Ntip == 1)
-        stop("found only one tip in the tree!")
-    Nedge <- dim(x$edge)[1]
-    if (any(tabulate(x$edge[, 1]) == 1))
-        stop("there are single (non-splitting) nodes in your tree; you may need to use collapse.singles().")
-    Nnode <- x$Nnode
-    if (is.null(x$edge.length)) use.edge.length <- FALSE
-    phyloORclado <- type %in% c("phylogram", "cladogram")
-    horizontal <- direction %in% c("rightwards", "leftwards")
-    if (phyloORclado) {
-        if (!is.null(attr(x, "order")))
-            if (attr(x, "order") == "pruningwise")
-                x <- reorder(x)
-        yy <- numeric(Ntip + Nnode)
-        TIPS <- x$edge[x$edge[, 2] <= Ntip, 2]
-        yy[TIPS] <- 1:Ntip
-
-    }
-
-    xe <- x$edge
-    x <- reorder(x, order = "pruningwise")
-    ereorder <- match(x$edge[, 2], xe[, 2])
-
-    if (phyloORclado) {
-        if (is.null(node.pos)) {
-            node.pos <- 1
-            if (type == "cladogram" && !use.edge.length)
-                node.pos <- 2
-        }
-        if (node.pos == 1)
-            yy <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
-                as.integer(x$edge[, 1]), as.integer(x$edge[,
-                  2]), as.integer(Nedge), as.double(yy), DUP = FALSE,
-                PACKAGE = "ape")[[6]]
-        else {
-            ans <- .C("node_height_clado", as.integer(Ntip),
-                as.integer(Nnode), as.integer(x$edge[, 1]), as.integer(x$edge[,
-                  2]), as.integer(Nedge), double(Ntip + Nnode),
-                as.double(yy), DUP = FALSE, PACKAGE = "ape")
-            xx <- ans[[6]] - 1
-            yy <- ans[[7]]
-        }
-        if (!use.edge.length) {
-            if (node.pos != 2)
-                xx <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-                  as.integer(x$edge[, 1]), as.integer(x$edge[,
-                    2]), as.integer(Nedge), double(Ntip + Nnode),
-                  DUP = FALSE, PACKAGE = "ape")[[6]] - 1
-            xx <- max(xx) - xx
-        }
-        else {
-            xx <- .C("node_depth_edgelength", as.integer(Ntip),
-                as.integer(Nnode), as.integer(x$edge[, 1]), as.integer(x$edge[,
-                  2]), as.integer(Nedge), as.double(x$edge.length),
-                double(Ntip + Nnode), DUP = FALSE, PACKAGE = "ape")[[7]]
-        }
-    }
-    ##if (type == "fan") {
-    ##    TIPS <- xe[which(xe[, 2] <= Ntip), 2]
-    ##    xx <- seq(0, 2 * pi * (1 - 1/Ntip), 2 * pi/Ntip)
-    ##    theta <- double(Ntip)
-    ##    theta[TIPS] <- xx
-    ##    theta <- c(theta, numeric(Nnode))
-    ##    theta <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
-    ##        as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-    ##        as.integer(Nedge), theta, DUP = FALSE, PACKAGE = "ape")[[6]]
-    ##    if (use.edge.length) {
-    ##        r <- .C("node_depth_edgelength", as.integer(Ntip),
-    ##            as.integer(Nnode), as.integer(x$edge[, 1]), as.integer(x$edge[,
-    ##              2]), as.integer(Nedge), as.double(x$edge.length),
-    ##            double(Ntip + Nnode), DUP = FALSE, PACKAGE = "ape")[[7]]
-    ##    }
-    ##    else {
-    ##        r <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-    ##            as.integer(x$edge[, 1]), as.integer(x$edge[,
-    ##              2]), as.integer(Nedge), double(Ntip + Nnode),
-    ##            DUP = FALSE, PACKAGE = "ape")[[6]]
-    ##        r <- 1/r
-    ##    }
-    ##    xx <- r * cos(theta)
-    ##    yy <- r * sin(theta)
-    ##}
-    ##if (type == "unrooted") {
-    ##    XY <- if (use.edge.length)
-    ##        unrooted.xy(Ntip, Nnode, x$edge, x$edge.length)
-    ##    else unrooted.xy(Ntip, Nnode, x$edge, rep(1, Nedge))
-    ##    xx <- XY$M[, 1] - min(XY$M[, 1])
-    ##    yy <- XY$M[, 2] - min(XY$M[, 2])
-    ##}
-    ##if (type == "radial") {
-    ##    X <- .C("node_depth", as.integer(Ntip), as.integer(Nnode),
-    ##        as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-    ##        as.integer(Nedge), double(Ntip + Nnode), DUP = FALSE,
-    ##        PACKAGE = "ape")[[6]]
-    ##    X[X == 1] <- 0
-    ##    X <- 1 - X/Ntip
-    ##    yy <- c((1:Ntip) * 2 * pi/Ntip, rep(0, Nnode))
-    ##    Y <- .C("node_height", as.integer(Ntip), as.integer(Nnode),
-    ##        as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
-    ##        as.integer(Nedge), as.double(yy), DUP = FALSE, PACKAGE = "ape")[[6]]
-    ##    xx <- X * cos(Y)
-    ##    yy <- X * sin(Y)
-    ##}
-    if (phyloORclado && direction != "rightwards") {
-        if (direction == "leftwards") {
-            xx <- -xx
-            xx <- xx - min(xx)
-        }
-        if (!horizontal) {
-            tmp <- yy
-            yy <- xx
-            xx <- tmp - min(tmp) + 1
-            if (direction == "downwards") {
-                yy <- -yy
-                yy <- yy - min(yy)
-            }
-        }
-    }
-    cbind(xx, yy)
-}